Back on January 4th, we reported Google Not Showing Localized Pages Within Country For .COM TLDs. We have specific examples showing that Google was not showing proper pages for .com domains, when one conducts a site command search, but restricts that search to a origin.
It appears based on Matt Cutts's Infrastructure status, January 2007 post that this should be resolved soon or even now.
I thought we’d nailed this issue in December, but we found another way that this can happen. I believe a fix has been submitted and is percolating its way through the system. Of the ~7 examples that I know of, I believe all but one is working now (and the remaining site is doing a chain of like five 302 redirects to weird/long/deep urls). However, if you 1) have a .com that is hosted outside the US, 2) searching on (say) google.co.uk for [site:yourdomain.com] returns your root page and all your pages for “Search the web”, 3) if you switch to (say) “pages from the UK”, the root page does not appear but the rest of your pages do, then this paragraph applies to you. I’d wait 4-5 days to let this second change percolate completely into our index, and if you still see the behavior after 4-5 days, please leave a comment with the name of your site.
So it has been 5 days since his post on this and we do see some improvements, but not all sites are yet a 100%, as far as I can tell.
SEOptimise tells his story, being a .com hosted in a UK data center.
Discussion at WebmasterWorld has others noticing that this isn't 100% right just yet. Discussion at Search Engine Roundtable Forums says it has been resolved for many cases.

Comments:
Kelvin Jones
01/19/2007 01:26 pm
I have a site, bumptobaby.org, which is a .org and is showing the above symptoms. Search the WEB: http://www.google.co.uk/search?hl=en&safe=off&q=site%3Awww.bumptobaby.org&btnG=Search&meta= Search pages from UK: http://www.google.co.uk/search?hl=en&safe=off&q=site%3Awww.bumptobaby.org&btnG=Search&meta=cr%3DcountryUK%7CcountryGB It would be nice to know how we can help GoogleBot figure out that this is a UK site.
Matt Cutts
01/24/2007 05:46 am
Kelvin Jones, you appear to have a different issue. Instead of just the root page not showing, none of your pages are showing. That seems to indicate that we don't think the IP address is in the UK. The IP address of bumptobaby.org is 64.13.192.148, and it looks like several web-based geolocation services think that IP is in the US. So I don't think you have the issue that we've been talking about.
Barry Schwartz
01/24/2007 10:51 am
Thanks Matt!
Nikhil
01/26/2007 03:26 am
I'm still seeing heaps of sites suffering from this problem. In the UK, there's: www.w1office.com www.awkspc.com www.awkspcrepairs.com www.sportsinjurybulletin.com www.companypartners.com www.thechildrensfurniturecompany.com www.bombaybedspread.com www.simplyclicks.com www.floorheatingonline.com www.warburtech.com www.columbusdt.com www.dekassa.com www.reachsanta.com www.theweddingsinger.uk.com not to mention my own site (which is in Australia, not UK). These were all collected from the one thread on MC's blog, as well as the Google groups thread linked to from the blog post.
Nikhil
01/28/2007 07:20 am
Let's not forget australia.com <a href="http://www.google.com.au/search?q=australia&sourceid=navclient-ff&ie=UTF-8&rlz=1B3GGGL_enAU205AU205" rel="nofollow">here</a> - now choose "Pages from Australia". Rather ridiculous when Google can't recognise "australia.com" as Australian.
sam
02/19/2007 05:46 pm
Our site was re-included in the google.co.uk (pages from within the uk search) last week. This week it is gone again. Furthermore, the url is displaying without 'www' in front of it. Please help!